Starting phenix.real_space_refine on Tue Nov 14 16:19:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/11_2023/8c91_16498.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/11_2023/8c91_16498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/11_2023/8c91_16498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/11_2023/8c91_16498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/11_2023/8c91_16498.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c91_16498/11_2023/8c91_16498.pdb" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.082 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2077 5.49 5 S 41 5.16 5 C 28981 2.51 5 N 11042 2.21 5 O 16969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 59110 Number of models: 1 Model: "" Number of chains: 18 Chain: "C" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1195 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 10, 'TRANS': 145} Chain breaks: 1 Chain: "D" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1348 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 175} Chain breaks: 1 Chain: "E" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1461 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 1 Chain: "J" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1121 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Chain: "K" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 929 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain breaks: 1 Chain: "L" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 769 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 1 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Chain: "T" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 730 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "2" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 315 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "A" Number of atoms: 44635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2077, 44635 Classifications: {'RNA': 2077} Modifications used: {'rna2p_pur': 200, 'rna2p_pyr': 108, 'rna3p_pur': 1021, 'rna3p_pyr': 748} Link IDs: {'rna2p': 308, 'rna3p': 1768} Chain breaks: 5 Time building chain proxies: 22.52, per 1000 atoms: 0.38 Number of scatterers: 59110 At special positions: 0 Unit cell: (170, 203.75, 203.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 2077 15.00 O 16969 8.00 N 11042 7.00 C 28981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.03 Conformation dependent library (CDL) restraints added in 2.7 seconds 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3414 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 27 sheets defined 31.5% alpha, 18.8% beta 678 base pairs and 1000 stacking pairs defined. Time for finding SS restraints: 20.54 Creating SS restraints... Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 61 through 72 Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.295A pdb=" N ASP D 103 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 25 through 40 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 154 through 160 removed outlier: 4.083A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.886A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 11 Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.687A pdb=" N LYS J 61 " --> pdb=" O ASN J 58 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL J 62 " --> pdb=" O ALA J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 58 through 62' Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 96 through 109 removed outlier: 4.168A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 120 Processing helix chain 'J' and resid 131 through 136 removed outlier: 4.374A pdb=" N ALA J 134 " --> pdb=" O ASN J 131 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 111 No H-bonds generated for 'chain 'K' and resid 109 through 111' Processing helix chain 'K' and resid 112 through 117 removed outlier: 3.957A pdb=" N SER K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 33 removed outlier: 3.782A pdb=" N GLY L 32 " --> pdb=" O LYS L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 94 through 99 Processing helix chain 'L' and resid 135 through 139 Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 55 removed outlier: 4.779A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 68 Processing helix chain 'N' and resid 72 through 79 Processing helix chain 'N' and resid 82 through 89 removed outlier: 4.584A pdb=" N SER N 89 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 11 removed outlier: 3.676A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 55 removed outlier: 3.585A pdb=" N HIS P 55 " --> pdb=" O ARG P 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 52 through 55' Processing helix chain 'P' and resid 96 through 102 removed outlier: 4.011A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU P 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG P 102 " --> pdb=" O LEU P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 107 Processing helix chain 'Q' and resid 5 through 20 removed outlier: 3.637A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 29 removed outlier: 4.383A pdb=" N ARG Q 27 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 72 removed outlier: 4.078A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 115 removed outlier: 3.637A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 25 removed outlier: 3.777A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.879A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 62 removed outlier: 4.377A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 removed outlier: 3.543A pdb=" N LEU S 69 " --> pdb=" O ILE S 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 10 removed outlier: 3.660A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'Y' and resid 2 through 7 Processing helix chain 'Y' and resid 9 through 32 removed outlier: 3.843A pdb=" N GLN Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 56 removed outlier: 3.680A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 42 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG Y 47 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG Y 48 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 16 removed outlier: 3.670A pdb=" N ARG 0 12 " --> pdb=" O THR 0 8 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 24 removed outlier: 3.971A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 removed outlier: 3.898A pdb=" N ARG 2 28 " --> pdb=" O THR 2 24 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN 2 29 " --> pdb=" O LYS 2 25 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing sheet with id=AA1, first strand: chain 'C' and resid 100 through 104 removed outlier: 7.011A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 128 through 130 Processing sheet with id=AA3, first strand: chain 'C' and resid 162 through 163 Processing sheet with id=AA4, first strand: chain 'D' and resid 21 through 28 removed outlier: 6.866A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 80 through 83 removed outlier: 3.589A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN D 32 " --> pdb=" O ILE D 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 117 through 118 removed outlier: 4.052A pdb=" N GLY D 117 " --> pdb=" O MET D 165 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET D 165 " --> pdb=" O GLY D 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 180 through 181 Processing sheet with id=AA8, first strand: chain 'E' and resid 2 through 3 removed outlier: 4.242A pdb=" N LEU E 3 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU E 12 " --> pdb=" O LEU E 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.828A pdb=" N ASP E 168 " --> pdb=" O VAL E 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.602A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 74 through 76 removed outlier: 4.250A pdb=" N TYR J 74 " --> pdb=" O ALA J 87 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA J 87 " --> pdb=" O TYR J 74 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS J 76 " --> pdb=" O LYS J 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 7 through 10 removed outlier: 3.517A pdb=" N LEU K 8 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.637A pdb=" N VAL K 69 " --> pdb=" O ILE K 77 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG P 87 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU P 26 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL P 85 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LYS P 28 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE P 83 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N TRP P 30 " --> pdb=" O ASP P 81 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASP P 81 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.518A pdb=" N GLU N 114 " --> pdb=" O ARG N 96 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.759A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.736A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 19 through 23 removed outlier: 3.946A pdb=" N VAL R 20 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL R 96 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP R 95 " --> pdb=" O ALA R 65 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS R 97 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL R 63 " --> pdb=" O LYS R 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.344A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 3 through 10 removed outlier: 5.483A pdb=" N ILE S 4 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL S 107 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.849A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N VAL T 31 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP T 80 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL T 62 " --> pdb=" O TRP T 80 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS T 82 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N THR T 60 " --> pdb=" O LYS T 82 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR T 84 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL T 58 " --> pdb=" O TYR T 84 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR T 86 " --> pdb=" O GLU T 56 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'T' and resid 67 through 68 Processing sheet with id=AC4, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.402A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE U 72 " --> pdb=" O GLU U 9 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN U 73 " --> pdb=" O LYS U 78 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS U 78 " --> pdb=" O ASN U 73 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 40 through 44 Processing sheet with id=AC6, first strand: chain 'U' and resid 83 through 86 Processing sheet with id=AC7, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AC8, first strand: chain '0' and resid 47 through 48 removed outlier: 3.667A pdb=" N TYR 0 48 " --> pdb=" O ARG 0 51 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 35 through 38 494 hydrogen bonds defined for protein. 1371 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1723 hydrogen bonds 2784 hydrogen bond angles 0 basepair planarities 678 basepair parallelities 1000 stacking parallelities Total time for adding SS restraints: 67.57 Time building geometry restraints manager: 27.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8654 1.33 - 1.45: 27776 1.45 - 1.57: 23988 1.57 - 1.69: 4148 1.69 - 1.81: 78 Bond restraints: 64644 Sorted by residual: bond pdb=" O5' A A1566 " pdb=" C5' A A1566 " ideal model delta sigma weight residual 1.424 1.453 -0.029 1.50e-02 4.44e+03 3.62e+00 bond pdb=" N GLU T 4 " pdb=" CA GLU T 4 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.41e+00 bond pdb=" N MET K 1 " pdb=" CA MET K 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.18e+00 bond pdb=" N ILE T 2 " pdb=" CA ILE T 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.06e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.04e+00 ... (remaining 64639 not shown) Histogram of bond angle deviations from ideal: 97.70 - 104.96: 9405 104.96 - 112.21: 37260 112.21 - 119.46: 21348 119.46 - 126.71: 23621 126.71 - 133.97: 5989 Bond angle restraints: 97623 Sorted by residual: angle pdb=" C3' A A1566 " pdb=" C2' A A1566 " pdb=" C1' A A1566 " ideal model delta sigma weight residual 101.50 97.70 3.80 1.00e+00 1.00e+00 1.44e+01 angle pdb=" N ALA E 161 " pdb=" CA ALA E 161 " pdb=" C ALA E 161 " ideal model delta sigma weight residual 114.62 110.72 3.90 1.14e+00 7.69e-01 1.17e+01 angle pdb=" CA ALA E 161 " pdb=" C ALA E 161 " pdb=" N ARG E 162 " ideal model delta sigma weight residual 119.71 116.36 3.35 1.17e+00 7.31e-01 8.18e+00 angle pdb=" N ARG T 3 " pdb=" CA ARG T 3 " pdb=" C ARG T 3 " ideal model delta sigma weight residual 113.29 107.84 5.45 2.00e+00 2.50e-01 7.43e+00 angle pdb=" O ARG T 3 " pdb=" C ARG T 3 " pdb=" N GLU T 4 " ideal model delta sigma weight residual 121.88 124.75 -2.87 1.07e+00 8.73e-01 7.18e+00 ... (remaining 97618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 33000 34.78 - 69.57: 894 69.57 - 104.35: 80 104.35 - 139.14: 12 139.14 - 173.92: 6 Dihedral angle restraints: 33992 sinusoidal: 28710 harmonic: 5282 Sorted by residual: dihedral pdb=" O4' U A1174 " pdb=" C1' U A1174 " pdb=" N1 U A1174 " pdb=" C2 U A1174 " ideal model delta sinusoidal sigma weight residual 200.00 41.18 158.82 1 1.50e+01 4.44e-03 8.24e+01 dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 53.21 146.79 1 1.50e+01 4.44e-03 7.84e+01 dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual -128.00 45.92 -173.92 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 33989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 12403 0.084 - 0.167: 226 0.167 - 0.251: 1 0.251 - 0.334: 0 0.334 - 0.418: 1 Chirality restraints: 12631 Sorted by residual: chirality pdb=" P A A1566 " pdb=" OP1 A A1566 " pdb=" OP2 A A1566 " pdb=" O5' A A1566 " both_signs ideal model delta sigma weight residual True 2.41 -2.83 -0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CA ILE T 2 " pdb=" N ILE T 2 " pdb=" C ILE T 2 " pdb=" CB ILE T 2 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" CA ILE S 103 " pdb=" N ILE S 103 " pdb=" C ILE S 103 " pdb=" CB ILE S 103 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.42e-01 ... (remaining 12628 not shown) Planarity restraints: 4596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A 32 " -0.003 2.00e-02 2.50e+03 1.45e-02 4.74e+00 pdb=" N1 C A 32 " 0.006 2.00e-02 2.50e+03 pdb=" C2 C A 32 " 0.035 2.00e-02 2.50e+03 pdb=" O2 C A 32 " -0.022 2.00e-02 2.50e+03 pdb=" N3 C A 32 " -0.005 2.00e-02 2.50e+03 pdb=" C4 C A 32 " 0.005 2.00e-02 2.50e+03 pdb=" N4 C A 32 " -0.003 2.00e-02 2.50e+03 pdb=" C5 C A 32 " -0.007 2.00e-02 2.50e+03 pdb=" C6 C A 32 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A1351 " 0.001 2.00e-02 2.50e+03 1.26e-02 3.57e+00 pdb=" N1 C A1351 " -0.011 2.00e-02 2.50e+03 pdb=" C2 C A1351 " 0.021 2.00e-02 2.50e+03 pdb=" O2 C A1351 " 0.000 2.00e-02 2.50e+03 pdb=" N3 C A1351 " -0.024 2.00e-02 2.50e+03 pdb=" C4 C A1351 " 0.017 2.00e-02 2.50e+03 pdb=" N4 C A1351 " -0.002 2.00e-02 2.50e+03 pdb=" C5 C A1351 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C A1351 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 175 " 0.018 2.00e-02 2.50e+03 1.07e-02 3.42e+00 pdb=" N9 G A 175 " -0.022 2.00e-02 2.50e+03 pdb=" C8 G A 175 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G A 175 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G A 175 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A 175 " 0.013 2.00e-02 2.50e+03 pdb=" O6 G A 175 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G A 175 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A 175 " 0.014 2.00e-02 2.50e+03 pdb=" N2 G A 175 " -0.009 2.00e-02 2.50e+03 pdb=" N3 G A 175 " -0.004 2.00e-02 2.50e+03 pdb=" C4 G A 175 " -0.005 2.00e-02 2.50e+03 ... (remaining 4593 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 442 2.50 - 3.10: 40295 3.10 - 3.70: 110989 3.70 - 4.30: 155656 4.30 - 4.90: 213311 Nonbonded interactions: 520693 Sorted by model distance: nonbonded pdb=" O2' C A1462 " pdb=" O2' G A2702 " model vdw 1.896 2.440 nonbonded pdb=" O2' G A 175 " pdb=" O5' A A 176 " model vdw 1.898 2.440 nonbonded pdb=" O2' C A1351 " pdb=" O2' A A1571 " model vdw 1.914 2.440 nonbonded pdb=" O2' G A 636 " pdb=" O2' G A 638 " model vdw 1.925 2.440 nonbonded pdb=" O2' A A 299 " pdb=" O4' A A 300 " model vdw 1.937 2.440 ... (remaining 520688 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 7.590 Check model and map are aligned: 0.630 Set scattering table: 0.400 Process input model: 177.510 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.034 64644 Z= 0.082 Angle : 0.357 5.830 97623 Z= 0.186 Chirality : 0.025 0.418 12631 Planarity : 0.002 0.029 4596 Dihedral : 12.732 173.924 30578 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.75 % Favored : 96.08 % Rotamer: Outliers : 0.07 % Allowed : 2.24 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.20), residues: 1812 helix: 1.76 (0.25), residues: 504 sheet: 0.49 (0.31), residues: 309 loop : -0.59 (0.20), residues: 999 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 362 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 363 average time/residue: 0.6308 time to fit residues: 371.6910 Evaluate side-chains 229 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 2.253 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4066 time to fit residues: 3.0437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 20.0000 chunk 293 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 197 optimal weight: 10.0000 chunk 156 optimal weight: 10.0000 chunk 303 optimal weight: 20.0000 chunk 117 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 351 optimal weight: 20.0000 overall best weight: 9.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS K 88 ASN L 99 ASN P 40 GLN Q 19 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 HIS Y 20 ASN 0 18 HIS 2 29 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.252 64644 Z= 0.364 Angle : 0.774 14.515 97623 Z= 0.386 Chirality : 0.038 0.232 12631 Planarity : 0.007 0.149 4596 Dihedral : 14.676 174.019 26954 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 28.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.73 % Favored : 93.16 % Rotamer: Outliers : 0.20 % Allowed : 5.61 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.19), residues: 1812 helix: 0.24 (0.22), residues: 511 sheet: -0.40 (0.28), residues: 356 loop : -1.05 (0.19), residues: 945 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 274 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 277 average time/residue: 0.6226 time to fit residues: 284.0221 Evaluate side-chains 204 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 2.236 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4083 time to fit residues: 3.8075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 292 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 352 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 313 optimal weight: 20.0000 chunk 349 optimal weight: 30.0000 chunk 120 optimal weight: 5.9990 chunk 282 optimal weight: 10.0000 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 77 HIS ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 64644 Z= 0.276 Angle : 0.608 11.180 97623 Z= 0.308 Chirality : 0.033 0.231 12631 Planarity : 0.005 0.097 4596 Dihedral : 14.837 177.469 26954 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.96 % Favored : 93.93 % Rotamer: Outliers : 0.13 % Allowed : 4.75 % Favored : 95.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.19), residues: 1812 helix: 0.30 (0.23), residues: 515 sheet: -0.47 (0.27), residues: 372 loop : -1.21 (0.19), residues: 925 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 263 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 265 average time/residue: 0.5913 time to fit residues: 261.1485 Evaluate side-chains 210 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 209 time to evaluate : 2.243 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4139 time to fit residues: 3.0214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 347 optimal weight: 40.0000 chunk 264 optimal weight: 20.0000 chunk 182 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 236 optimal weight: 20.0000 chunk 353 optimal weight: 9.9990 chunk 374 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 334 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 overall best weight: 9.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN K 9 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS T 70 HIS ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 64644 Z= 0.345 Angle : 0.713 13.515 97623 Z= 0.361 Chirality : 0.038 0.283 12631 Planarity : 0.006 0.132 4596 Dihedral : 15.695 179.292 26954 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 31.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.89 % Favored : 92.00 % Rotamer: Outliers : 0.26 % Allowed : 5.74 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.19), residues: 1812 helix: -0.01 (0.22), residues: 514 sheet: -0.85 (0.28), residues: 349 loop : -1.52 (0.18), residues: 949 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 252 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 256 average time/residue: 0.5772 time to fit residues: 249.6342 Evaluate side-chains 203 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 202 time to evaluate : 2.253 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4084 time to fit residues: 3.0502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 311 optimal weight: 10.0000 chunk 212 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 278 optimal weight: 30.0000 chunk 154 optimal weight: 1.9990 chunk 319 optimal weight: 10.0000 chunk 258 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 335 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 overall best weight: 7.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN Q 19 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 HIS 0 4 GLN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.6369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 64644 Z= 0.293 Angle : 0.637 11.218 97623 Z= 0.324 Chirality : 0.035 0.272 12631 Planarity : 0.005 0.098 4596 Dihedral : 15.743 179.789 26954 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 28.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.67 % Favored : 92.22 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.19), residues: 1812 helix: 0.13 (0.23), residues: 504 sheet: -1.07 (0.27), residues: 370 loop : -1.51 (0.19), residues: 938 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.5747 time to fit residues: 255.5152 Evaluate side-chains 203 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.269 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 125 optimal weight: 4.9990 chunk 336 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 219 optimal weight: 50.0000 chunk 92 optimal weight: 5.9990 chunk 374 optimal weight: 20.0000 chunk 310 optimal weight: 10.0000 chunk 173 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 196 optimal weight: 40.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 ASN E 9 GLN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 86 GLN K 3 GLN K 9 ASN P 40 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN 0 18 HIS 2 26 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 64644 Z= 0.200 Angle : 0.558 11.940 97623 Z= 0.283 Chirality : 0.031 0.263 12631 Planarity : 0.004 0.111 4596 Dihedral : 15.424 178.622 26954 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.17 % Favored : 92.72 % Rotamer: Outliers : 0.07 % Allowed : 3.30 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.19), residues: 1812 helix: 0.41 (0.23), residues: 505 sheet: -0.99 (0.26), residues: 388 loop : -1.45 (0.19), residues: 919 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 280 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 280 average time/residue: 0.5606 time to fit residues: 268.7727 Evaluate side-chains 213 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.289 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 361 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 213 optimal weight: 10.0000 chunk 273 optimal weight: 20.0000 chunk 211 optimal weight: 10.0000 chunk 315 optimal weight: 30.0000 chunk 209 optimal weight: 20.0000 chunk 373 optimal weight: 40.0000 chunk 233 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 overall best weight: 9.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 167 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN P 74 GLN Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 39 GLN 0 18 HIS ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.7048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 64644 Z= 0.355 Angle : 0.714 12.009 97623 Z= 0.360 Chirality : 0.038 0.296 12631 Planarity : 0.006 0.122 4596 Dihedral : 16.198 176.511 26954 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 33.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.44 % Favored : 90.45 % Rotamer: Outliers : 0.07 % Allowed : 2.51 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.19), residues: 1812 helix: -0.07 (0.23), residues: 511 sheet: -1.35 (0.27), residues: 351 loop : -1.79 (0.19), residues: 950 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 245 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.5631 time to fit residues: 237.2117 Evaluate side-chains 193 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.279 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 230 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 222 optimal weight: 40.0000 chunk 112 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 254 optimal weight: 40.0000 chunk 184 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 167 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 ASN ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN K 90 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.6880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 64644 Z= 0.217 Angle : 0.579 12.306 97623 Z= 0.294 Chirality : 0.033 0.283 12631 Planarity : 0.005 0.107 4596 Dihedral : 15.790 179.136 26954 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 24.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.89 % Favored : 92.00 % Rotamer: Outliers : 0.07 % Allowed : 1.45 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.19), residues: 1812 helix: 0.28 (0.23), residues: 504 sheet: -1.22 (0.26), residues: 365 loop : -1.63 (0.19), residues: 943 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 255 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 255 average time/residue: 0.5697 time to fit residues: 250.1016 Evaluate side-chains 203 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.273 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 339 optimal weight: 20.0000 chunk 357 optimal weight: 20.0000 chunk 326 optimal weight: 20.0000 chunk 347 optimal weight: 40.0000 chunk 209 optimal weight: 20.0000 chunk 151 optimal weight: 6.9990 chunk 272 optimal weight: 30.0000 chunk 106 optimal weight: 3.9990 chunk 314 optimal weight: 20.0000 chunk 328 optimal weight: 20.0000 chunk 346 optimal weight: 30.0000 overall best weight: 14.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN Q 36 GLN Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.8042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 64644 Z= 0.507 Angle : 0.907 15.024 97623 Z= 0.451 Chirality : 0.047 0.347 12631 Planarity : 0.007 0.110 4596 Dihedral : 17.232 172.697 26954 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 46.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.65 % Favored : 89.18 % Rotamer: Outliers : 0.07 % Allowed : 1.39 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.18), residues: 1812 helix: -0.51 (0.22), residues: 505 sheet: -1.84 (0.27), residues: 335 loop : -2.02 (0.18), residues: 972 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.5956 time to fit residues: 229.5201 Evaluate side-chains 183 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 2.315 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 228 optimal weight: 10.0000 chunk 367 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 174 optimal weight: 7.9990 chunk 255 optimal weight: 30.0000 chunk 385 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 chunk 307 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 237 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 overall best weight: 9.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 18 HIS ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.7913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 64644 Z= 0.339 Angle : 0.710 12.793 97623 Z= 0.358 Chirality : 0.038 0.348 12631 Planarity : 0.006 0.119 4596 Dihedral : 16.823 177.990 26954 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 33.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.60 % Favored : 90.29 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.18), residues: 1812 helix: -0.28 (0.22), residues: 507 sheet: -1.73 (0.26), residues: 337 loop : -2.04 (0.18), residues: 968 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3624 Ramachandran restraints generated. 1812 Oldfield, 0 Emsley, 1812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.5543 time to fit residues: 229.7968 Evaluate side-chains 192 residues out of total 1516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 2.750 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 243 optimal weight: 30.0000 chunk 327 optimal weight: 10.9990 chunk 94 optimal weight: 0.5980 chunk 283 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 307 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 315 optimal weight: 30.0000 chunk 38 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 overall best weight: 7.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN ** E 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN Q 43 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.056253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.042221 restraints weight = 556077.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.043045 restraints weight = 244281.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.043598 restraints weight = 158024.321| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.7852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 64644 Z= 0.272 Angle : 0.644 11.854 97623 Z= 0.325 Chirality : 0.035 0.317 12631 Planarity : 0.005 0.102 4596 Dihedral : 16.530 179.478 26954 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 29.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.49 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.18), residues: 1812 helix: 0.02 (0.23), residues: 502 sheet: -1.60 (0.26), residues: 342 loop : -2.03 (0.18), residues: 968 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6353.95 seconds wall clock time: 118 minutes 7.53 seconds (7087.53 seconds total)